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Archive for New OCB Research

A Microbial Conveyor Belt Beneath the South Pacific

Posted by mmaheigan

· Friday, October 17th, 2025

Global overturning circulation is a planetary conveyor belt: dense waters sink around Antarctica, spread through the deep ocean for centuries, and eventually rise elsewhere, redistributing heat, nutrients, and carbon. But how does this slow, pervasive movement of water impact marine microbes?

To find out, researchers collected over 300 water samples spanning the full depth of the ocean along the GO-SHIP P18 line in the South Pacific. They found that microbial genomes cluster into six spatial cohorts that are not only delineated by depth, but also circulatory features, like Antarctic Bottom Water formation, and ventilation age. Distinct functional signatures also emerged across these circulation-driven zones. For example, genes for light harvesting and iron uptake dominate in surface waters, while adaptations for cold, high pressure, or anaerobic metabolism characterize deep and ancient waters. Antarctic Bottom Water communities also carry hallmarks of rapid genetic exchange, suggesting horizontal gene transfer may help microbes adapt as they sink into the deep ocean. Even in waters isolated from the atmosphere for over a thousand years, many microbial genomes have coverage patterns that imply active replication, demonstrating that long-isolated water masses still support active microbial populations. In considering patterns of microbial diversity, researchers also identified a pervasive “prokaryotic phylocline” in which richness spikes just below the surface mixed layer and remains high to full ocean depth, only dipping slightly in very old water.

These results demonstrate that physical circulation, not just temperature or nutrients, partitions the ocean into microbial biomes. Understanding this linkage is critical because microbes determine the amount of carbon that is recycled or stored long-term in the deep ocean. As climate change alters overturning circulation, the functioning of these hidden microbial ecosystems and their role in regulating atmospheric CO₂ may shift in unexpected ways.

Authors
Bethany C. Kolody (University of California San Diego; UC Berkeley; J. Craig Venter Institute)
Rohan Sachdeva (UC Berkeley)
Hong Zheng (J. Craig Venter Institute)
Zoltán Füssy (UC San Diego; J. Craig Venter Institute)
Eunice Tsang (UC Berkeley)
Rolf E. Sonnerup (University of Washington)
Sarah G. Purkey (UC San Diego)
Eric E. Allen (UC San Diego)
Jillian F. Banfield (UC Berkeley; Lawrence Berkeley National Laboratory; Monash University)
Andrew E. Allen (UC San Diego; JCVI)

Social media
Twitter/X: @science_doodles, @Scripps_Ocean, @JCVenterInst
Bluesky: @banfieldlab.bsky.social, @bethanykolody.bsky.social, @scrippsocean.bsky.social, @jcvi.org

https://www.science.org/doi/10.1126/science.adv6903
Overturning circulation structures the microbial functional seascape of the South Pacific
Science

Marine plant metabolites give marine microbes gas

Posted by mmaheigan

· Friday, October 17th, 2025

A recent study in Nature Geosciences observed high concentrations of methane overlying permeable (sand) sand sediments in bays in Denmark and Australia. These environments are not one would expect to see methane because they are highly oxygenated and the high concentrations of sulfate in seawater typically inhibit methanogenesis. The authors showed that the methane was not being imported from local groundwater using geochemical methods. Using a combination of biogeochemical, microbial isolation, culturing and genomic approaches, revealed that methane was being produced by fast growing microbes resistant to oxygen exposure using plant produced substrates such as dimethylsulfide and amines. This work shows that where marine plants such as seaweed and seagrass grow and accumulate there may be high and sporadic production of methane. This has implications for how we account for the carbon sequestering capacity of coastal environments and the climate impact of increasing algal blooms such as coastal Ulva and the great sargassum bloom.

Authors
Perran Cook (Monash University)
Ning Hall (University of free spirit)

From smoke to sea, how wildfire ash reshapes ocean microbial life

Posted by mmaheigan

· Friday, September 26th, 2025

When wildfire smoke drifts over the ocean, what happens beneath the waves? As wildfires change in nature and become more frequent, it’s increasingly important to understand how ash deposition affects the ocean’s smallest, yet most essential, inhabitants.

Figure 1. Conceptual illustration of coastal wildfires. Coarse-mode smoke including ash, rich in organic matter and low in minerals, is likely to settle near the fire source. Fine-mode smoke, with lower organic content and higher mineral composition, disperses farther. Wildfire smoke deposition can introduce both fertilizing nutrients, such as inorganic nitrogen and iron, and more toxic compounds, including dissolved organic matter (DOM) species like aromatic hydrocarbons, affecting marine trophic levels. Additionally, wildfire smoke on the ocean surface may alter sunlight penetration, impacting phytoplankton photosynthesis.

In a recent study, the authors investigated how wildfire ash leachate influences coastal microbial communities. Through field incubations along the California coast, we found that ash-derived dissolved organic matter (DOM) increased bacterioplankton specific growth rates and organic matter remineralization, while leaving bacterial growth efficiency unchanged. This suggests that the added DOM was primarily used to fuel basic cellular functions rather than biomass production. Meanwhile, microzooplankton grazing declined, even as phytoplankton division rates remained stable, hinting at a decoupling of predator-prey dynamics that could promote phytoplankton accumulation.

Pre-existing phytoplankton biomass had a greater influence on microbial responses than the chemical composition of the ash itself. In low-biomass waters, bacteria more readily consumed the ash-derived DOM. In contrast, in high-biomass waters, the leachate was less bioavailable, potentially allowing more refractory ash-derived carbon to accumulate. These baseline differences appeared to influence phytoplankton size structure: smaller cells increased in high-biomass settings, while larger cells became more prevalent in low-biomass waters. These shifts may have implications for nutrient cycling, food web structure, and carbon export pathways, depending on how microbial activity and community composition respond in situ.

Authors
Nicholas Baetge (Oregon State University)
Kimberly Halsey (Oregon State University)
Erin Hanan (University of Nevada, Reno)
Michael Behrenfeld (Oregon State University)
Allen Milligan (Oregon State University)
Jason Graff (Oregon State University)
Parker Hansen (Oregon State University)
Craig Carlson (University of California, Santa Barbara)
Rene Boiteau (University of Minnesota)
Eleanor Arrington (University of California, Santa Barbara)
Jacqueline Comstock (University of California, Santa Barbara)
Elisa Halewood (University of California, Santa Barbara)
Elizabeth Harvey (University of New Hampshire)
Norm Nelson (University of California, Santa Barbara)
Keri Opalk (University of California, Santa Barbara)
Brian Ver Wey (Oregon State University)

How does a persistent eddy impact the biological carbon pump?

Posted by mmaheigan

· Friday, September 26th, 2025

The Lofoten Basin Eddy (LBE) is a unique and persistent anticyclonic feature of the Norwegian Sea that stirs the water column year-round. However, its impact on biogeochemical processes that influence region carbon storage, including carbon fixation, particle aggregation and fragmentation, and remineralization, has remained largely unknown.

Figure caption: (a) Map of the Lofoten Basin Eddy study region including locations of 1886 profiles from 22 Biogeochemical-Argo floats (2010–2022) and a heatmap showing the relative extent of the LBE influence zone over the timeseries. (b–d) Mean monthly profiles and the difference (Δ) determined as inside minus outside the LBE influence zone of the mass concentration of particulate organic carbon in small particles (POC_s). Arrows indicate key mechanisms regulating the regional biological carbon.

Using 12 years of data from Biogeochemical-Argo floats and satellite altimetry to track eddy movements, Koestner et al. (2025) examined how the LBE influences the seasonal transport of organic carbon from surface waters to the deep ocean. While the LBE can enhance carbon export during certain months, like during spring shoaling and late autumn subduction, it generally reduces the efficiency of the biological carbon pump. Inside the eddy, warmer subsurface waters and slower-sinking particles often lead to more respiration and remineralization, meaning less carbon reached the deep sea.

The LBE’s persistent influence on organic carbon cycling could affect regional climate feedbacks and marine ecosystems, including key fisheries in Norway. Understanding how features like the LBE modulate carbon sequestration is vital for improving climate models and managing ocean resources in a warming Arctic.

Authors
Daniel Koestner (University of Bergen)
Sophie Clayton (National Oceanography Centre)
Paul Lerner (Columbia University)
Alexandra E. Jones-Kellett (MIT & WHOI)
Stevie L. Walker (University of Washington)

New software enables global ocean biogeochemical modeling in Python

Posted by mmaheigan

· Friday, September 5th, 2025

Have you ever wondered what life would be like if you could write and run complex biogeochemical models easily and conveniently in Python? Wonder no more. In a paper published in J. Adv. Model. Earth Syst., Samar Khatiwala (2025; see reference below) describes tmm4py, a new software to enable efficient, global scale biogeochemical modelling in Python.

tmm4py is based on the Transport Matrix Method (TMM), an efficient numerical scheme for “offline” simulation of tracers driven by circulations from state-of-the-art physical models and state estimates. tmm4py exposes this functionality in Python, providing the tools needed to implement complex models in pure Python using standard modules such as NumPy, and run them interactively on hardware ranging from laptops to supercomputers. No knowledge of parallel computing required! tmm4py even extends the interactivity to models written in Fortran, allowing the many existing models coupled to the TMM, e.g., MITgcm, to be used from the familiar comfort of Python. Whether you’re a seasoned modeler, just want to try out an idea, or illustrate a concept in your teaching, tmm4py is designed to make biogeochemical modeling more widely accessible.

Download the code from: https://github.com/samarkhatiwala/tmm

Figure: Schematic illustrating the structure of tmm4py and its relationship with the various libraries and components it is built on or interacts with. Outlined boxes represent user‐supplied code (such as the “Hello World” example of the ideal age tracer shown on the left). Other low-level libraries on which tmm4py depends, for example, BLAS and LAPACK for linear algebra, MPI for parallel communication, and CUDA for GPUs, are not shown.

Author
Samar Khatiwala (Waseda Univ)

Joint Science Highlight with GEOTRACES.

Migrating zooplankton increase N2 production in Oxygen Deficient Zones

Posted by mmaheigan

· Friday, August 15th, 2025

Diel Vertically Migrating Zooplankton that spend their day in an Oxygen Deficient Zone to avoid predators are a previously ignored source of organic matter for N₂ producing bacteria.

A recent study in GBC, examined biogeochemical cycling in the offshore Eastern Tropical North Pacific Oxygen Deficient Zone. They found that the daytime maximum in backscattering, used as a proxy for zooplankton and forage fish, corresponded to quantitative PCR maxima in zooplankton and forage fish (metazoan) DNA and to the maximum in biological N₂ gas, and a shoulder of the nitrite maximum. At the same time, the C:N ratio of both suspended and sinking organic matter were reduced, indicating less degraded organic matter. These data strongly suggest that N₂ production in the core of the Oxygen Deficient Zone is stimulated by the daily migration of zooplankton and forage fish in the Oxygen Deficient Zone. These results decouple N₂ production from sinking organic matter fluxes. This work indicates that multicellular animals can affect key ocean biogeochemical cycles, and can cause hot spots of microbial activity well below the sunlit ocean.

Figure caption: Offshore Eastern Tropical North Pacific Oxygen Deficient Zone. The dashed black line indicates the top of the ODZ, the gray lines indicate the boundaries of the deep vertical migration maximum. A) Concentrations of nitrite and oxygen, B) C:N of suspended and of sinking (sediment trap) organic matter, C) Day and night backscattering, a proxy for zooplankton and forage fish, and D) Biological N2 gas concentrations and day and night quantitative PCR data for zooplankton and forage fish (metazoans).

Authors
Clara Fuchsman (UMCES Horn Point Laboratory)
Megan Duffy (Univ Vermont)
Jacob Cram (UMCES Horn Point Laboratory)
Paulina Huanca-Valenzuela (UMCES Horn Point Laboratory)
Louis Plough (UMCES Horn Point Laboratory)
James Pierson (UMCES Horn Point Laboratory)
Catherine Fitzgerald (UMCES Horn Point Laboratory)
Allan Devol (U. of Washington)
Richard Keil (U. of Washington)

Paper: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2024GB008365

Giant iceberg meltwater supplies nutrients to upper ocean layers

Posted by mmaheigan

· Friday, August 15th, 2025

Iceberg meltwater induces mixing which erodes upper-ocean layers. This supplies nutrients, both released from the iceberg and entrained from deeper waters, to surface waters which stimulates phytoplankton growth.

Meltwater from the base, sidewalls and surface of giant icebergs influences upper ocean stratification and mixing. Containing a substantial micro-nutrient load, (incorporating nutrient-rich deep waters along with mineral-rich particles, such as iron and silica, from the melting iceberg), this meltwater is thought to relieve nutrient limitation in surface ecosystems, impacting ocean biological productivity and carbon drawdown. A recent paper in Nature Geoscience provides high-resolution glider measurements right next to giant iceberg A-68A; elucidating the effects of meltwater on water mass modification and near-surface productivity.

The number of calving icebergs is expected to increase in the near future, however the impact of iceberg meltwater on the hydrography, circulation and mixing of the upper ocean is poorly quantified. Understanding the complex physical and biological impacts on the ocean waters through which icebergs transit is difficult to represent in global ocean models, precipitating complexity in prediction of future ocean circulation and the health of Antarctic ecosystems.

Authors
Natasha S Lucas (British Antarctic Survey)
J. Alexander Brearley (British Antarctic Survey)
Katharine R Hendry (British Antarctic Survey)
Theo Spira (University of Gothenburg)
Anne Braakmann-Folgmann (The Arctic University of Norway)
E. Povl Abrahamsen (British Antarctic Survey)
Michael P Meredith (British Antarctic Survey)
Geraint A Tarling (British Antarctic Survey)

Social media:
@krhendry.bsky.social
@TashaOcean
www.bas.ac.uk
@britishantarcticsurvey
@bangor_university
@bangor.sos
@polarwomen @womeninoceanscience
#TashaGoesSouth #PolarResearch #SouthernOcean #AgulhasII #WomenInPhysics #WomenInScience #ExperimentalPhysics #Oceanography #Antarctica

A little extra background:

Roughly a quarter the size of Wales at 5800 square kilometres, A-68A was the biggest iceberg on Earth when it calved from the Larsen-C Ice Shelf in 2017. It arrived at South Georgia as the sixth largest giant iceberg on record. A-68A deposited an estimated 152 billion tonnes of nutrient-rich fresh water, equivalent to 61 million Olympic sized swimming pools, and 27 times the annual freshwater outflow from South Georgia, into the seas around this sub-Antarctic island during the three months of this glider survey.

Ocean gliders are a type of small, robotic underwater vehicle that use density differences, or buoyancy, to move up and down through the water column with wings to create lift, propelling it forward. While ‘flying’ through the water, from the surface to 1 km in depth, the gliders’ sensors measure the water’s properties. The glider surfaces at regular intervals to check its position by GPS, transmit sparse data back to the UK using a satellite phone system, and check for new instructions on where to go and what instruments to turn on.

Research Briefing https://rdcu.be/eg39r

Tracing the biological carbon pump across diverse export regimes

Posted by mmaheigan

· Thursday, May 29th, 2025

The ocean’s biological carbon pump (BCP) plays a crucial role in regulating Earth’s climate. But how efficiently does it transport carbon to the deep? It has been difficult to answer this question because observations are sparse, labor-intensive, and the uncertainties of the BCP’s magnitude, which are nearly equivalent to human emissions. Fortunately, autonomous vehicles unlock our ability to observe the upper ocean in three dimensions, garner a greater spatial and temporal range than a research vessel and, unlike a satellite, enable us to see into the deep.

Figure caption: This figure compares mean daily organic carbon flux (blue bars) with ship-based particulate organic carbon (POC) flux (purple bars) to show the different export regimes at 60 and 100 m depth at each study site (left panel: the subpolar northeast Pacific late summer; right panel: North Atlantic spring bloom. The inferred net DOC production (orange bars) was calculated as the difference between the organic carbon flux and the ship-based POC. At times, net community production (NCP, yellow bars) is smaller than the export terms, which suggests a contribution from earlier productivity to export that is consistent with the cruise period beginning on the tail end of a previous bloom. The error bars depict the 95% confidence interval.

A new paper in Limnology & Oceanography leverages these vehicles to autonomously characterize the BCP in two dramatically diverse carbon export regimes. The results reveal strong variability in carbon export efficiency, and further comparison with ship-based data informed the transport pathways. At the lower productivity site, nearly all of the carbon fixed by phytoplankton was routed into sinking particulate organic carbon, while at the highly productive site, nearly half was diverted to dissolved organic carbon. These insights refine our understanding of carbon transport processes and highlight the strength of multiple observational approaches used in tandem. This work is part of the NASA-led EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) program, that ultimately seeks to reduce the uncertainty in the global BCP through improved remote sensing algorithms.

Why does this matter? With climate change mitigation at the forefront of global policy, improving our understanding of the marine carbon cycle is essential. By providing continuous, high-resolution observations, autonomous platforms offer critical data to inform climate predictions, carbon sequestration strategies, and ocean conservation efforts.

Authors
Shawnee Traylor (MIT-WHOI Joint Program)
David P. Nicholson (Woods Hole Oceanographic Inst.)
Samantha J. Clevenger (MIT-WHOI Joint Program)
Ken O. Buesseler (Woods Hole Oceanographic Inst.)
Eric D’Asaro (Univ Washington)
Craig M. Lee (Univ Washington)

New over-determined CO2 system solver QUODcarb

Posted by mmaheigan

· Thursday, May 29th, 2025

Do you work with over-determined datasets of seawater carbon dioxide system chemistry? QUODcarb (Quantifying Uncertainty in an Over-Determined marine carbonate system), a new over-determined CO2-system solver is described in the recently published “QUODcarb: A Bayesian solver for over-determined datasets of seawater carbon dioxide system chemistry.” The Bayesian formulation of the novel solver and demonstrates its use on an over-determined dataset from the Gulf of Mexico (COMECC-3) that included measurements of DIC, AT, pH, pCO2, and [CO3]. The over-determined calculations, with self-consistent uncertainty quantification, can calculate carbonate ion concentration uncertainty within the GOA-ON climate uncertainty target of 1% with implications for ocean acidification monitoring projects.

Find the Matlab code on GitHub: https://github.com/fprimeau/QUODcarb

Figure caption: Diagram depicting the measured quantities (left side) and the use of thermodynamic constant (pK) formulations and mass balance total (_T) formulations in seawater carbonate chemistry calculations. Adapted from Figure 1 in Carter et al., 2024 a, to illustrate how QUODcarb can replace CO2SYS calculations to include three or more carbonate variable measurements in over-determined calculations while also enabling uncertainty quantification.
Physical measurements are shown with pink backgrounds, mass balance total contents are shown with light green backgrounds, thermodynamic constants are in gray, and carbonate chemistry variables are in yellow. Temperature dependent carbonate chemistry measurements (e.g., pH and pCO2) may be included at different input temperatures. The calculator reflects the analogy that QUODcarb acts as a calculator for solving the system of nonlinear equations.

Authors
Marina Fennell (University of California, Irvine)
Francois Primeau (University of California, Irvine)

Photoacclimation by phytoplankton under clouds

Posted by mmaheigan

· Thursday, May 29th, 2025

Unlike most remote sensing products, Net Primary Production (NPP) is computed under clouds. Since satellites can’t see through clouds, NPP models rely on clear-sky observations, interpolate model inputs, and assume that phytoplankton behavior stays the same, regardless of light conditions.

Figure caption: (a) Schematic of the photoacclimation process. In yellow, a standard photoacclimation curve where θ (the chlorophyll to phytoplankton carbon ratio), adjusts as a function of light in the mixed layer (Eg). In blue, the schematic when we do not consider photoacclimation under cloud: Eg is reduced due to cloud-cover, but θ remains the same as it was under cloud, resulting in a strongly reduced μ (a proxy for growth rate). When considering photoacclimation under clouds (red), θ increases because of a reduced Eg, resulting in a μcloudy(photo) > μcloudy(no photo). (b) Histogram of the distribution of θ*Eg (a proxy for growth rate) from BGC-Argo floats separated by whether under cloudy (red) or clear (yellow) skies.

But phytoplankton are known to photoacclimate, adjusting their internal chlorophyll to carbon ratio in response to changes in light. In this study published in GRL we used data from BGC-Argo floats to show that this acclimation occurs consistently under both clear and cloudy skies across the global ocean. Despite reduced light, phytoplankton maintain similar growth rates, suggesting that current estimates of NPP may be biased low when cloud cover is present.

Recognizing and correcting this bias could improve satellite-based NPP estimates, particularly in persistently cloudy regions like the Southern Ocean or eastern boundary upwelling zones. This, in turn, would refine models of the ocean’s biological carbon pump, leading to better projections of CO₂ uptake and export.

Authors
Charlotte Begouen Demeaux (Univ Maine)
Emmanuel Boss (Univ Maine)
Jason R. Graf (Oregon State Univ)
Michael J. Behrenfeld (Oregon State Univ)
Toby Westberry (Oregon State Univ)

Funding for the Ocean Carbon & Biogeochemistry Project Office is provided by the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA). The OCB Project Office is housed at the Woods Hole Oceanographic Institution.

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